Package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity

Class IntensityMeanShellBase

Object

AnchorBean<Feature<FeatureInputSingleObject>>

InitializableBean<Feature<FeatureInputSingleObject>,FeatureInitialization>

Feature<FeatureInputSingleObject>

FeatureSingleObject

FeatureEnergyChannel

IntensityMeanShellBase

Direct Known Subclasses:

IntensityMeanShell, IntensityMeanShellMaxSlice

public abstract class IntensityMeanShellBase
extends FeatureEnergyChannel

Constructs a shell around an object-mask using a standard dilation and erosion process.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
IntensityMeanShellBase()

Method Summary

Modifier and Type	Method	Description
protected double	calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input, Channel channel)	Calculates the feature value for a specific channel in the energy stack.
protected abstract double	calculateForShell(ObjectMask shell, Channel channel)	Calculates the feature value for the given shell and channel.
void	checkMisconfigured(BeanInstanceMap defaultInstances)	Checks that a bean's properties conform to expectations.
String	describeParameters()	A human-readable description of the parameterization of the bean.
double	getEmptyValue()	The value to return when the resulting object is empty.
int	getEnergyIndexMask()	A channel of the energyStack that is used as an additional mask using default byte values for on and off.
MorphologicalIterations	getIterations()	The number of dilations and erosions to apply and whether to do in the Z dimension.
boolean	isInverse()	If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
boolean	isInverseMask()	If true, uses the inverse of the passed mask.
void	setEmptyValue(double emptyValue)	The value to return when the resulting object is empty.
void	setEnergyIndexMask(int energyIndexMask)	A channel of the energyStack that is used as an additional mask using default byte values for on and off.
void	setInverse(boolean inverse)	If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).
void	setInverseMask(boolean inverseMask)	If true, uses the inverse of the passed mask.
void	setIterations(MorphologicalIterations iterations)	The number of dilations and erosions to apply and whether to do in the Z dimension.

Methods inherited from class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel

calculate, getEnergyIndex, setEnergyIndex

Methods inherited from class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject

inputType

Methods inherited from class org.anchoranalysis.feature.bean.Feature

assignTo, beforeCalc, calculateCheckInitialized, castAs, createListChildFeatures, describeBean, descriptionLong, duplicateChangeName, getCustomName, getFriendlyName, onInitialization, setCustomName, toString

Methods inherited from class org.anchoranalysis.bean.initializable.InitializableBean

getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized

Methods inherited from class org.anchoranalysis.bean.AnchorBean

describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

IntensityMeanShellBase

public IntensityMeanShellBase()

Method Details

checkMisconfigured

public void checkMisconfigured(BeanInstanceMap defaultInstances)
                        throws BeanMisconfiguredException

Description copied from class: AnchorBean

Checks that a bean's properties conform to expectations.

Overrides:

checkMisconfigured in class AnchorBean<Feature<FeatureInputSingleObject>>

Parameters:

defaultInstances - all available default instances if the DefaultInstance annotation is used

Throws:

BeanMisconfiguredException - if the bean has not been configured properly as XML

describeParameters

public String describeParameters()

Description copied from class: Feature

A human-readable description of the parameterization of the bean.

Overrides:

describeParameters in class Feature<FeatureInputSingleObject>

Returns:

the description.

calculateForChannel

protected double calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
 Channel channel)
                              throws FeatureCalculationException

Description copied from class: FeatureEnergyChannel

Calculates the feature value for a specific channel in the energy stack.

Specified by:

calculateForChannel in class FeatureEnergyChannel

Parameters:

input - the FeatureCalculationInput containing the FeatureInputSingleObject

channel - the Channel from the energy stack to calculate the feature on

Returns:

the calculated feature value

Throws:

FeatureCalculationException - if the calculation fails

calculateForShell

protected abstract double calculateForShell(ObjectMask shell,
 Channel channel)
                                     throws FeatureCalculationException

Calculates the feature value for the given shell and channel.

Parameters:

shell - the ObjectMask representing the shell

channel - the Channel to calculate the feature on

Returns:

the calculated feature value

Throws:

FeatureCalculationException - if the calculation fails

getIterations

public MorphologicalIterations getIterations()

The number of dilations and erosions to apply and whether to do in the Z dimension.

setIterations

public void setIterations(MorphologicalIterations iterations)

The number of dilations and erosions to apply and whether to do in the Z dimension.

isInverse

public boolean isInverse()

If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).

setInverse

public void setInverse(boolean inverse)

If true, calculates instead on the inverse of the object-mask (what's left when the shell is removed).

getEnergyIndexMask

public int getEnergyIndexMask()

A channel of the energyStack that is used as an additional mask using default byte values for on and off.

setEnergyIndexMask

public void setEnergyIndexMask(int energyIndexMask)

A channel of the energyStack that is used as an additional mask using default byte values for on and off.

isInverseMask

public boolean isInverseMask()

If true, uses the inverse of the passed mask.

setInverseMask

public void setInverseMask(boolean inverseMask)

If true, uses the inverse of the passed mask.

getEmptyValue

public double getEmptyValue()

The value to return when the resulting object is empty.

setEmptyValue

public void setEmptyValue(double emptyValue)

The value to return when the resulting object is empty.